[2026-05-28T22:36:10] Launching Arriba 2.4.0
[2026-05-28T22:36:10] Loading assembly from 'ref_genome.fa' 
[2026-05-28T22:36:23] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T22:36:28] Reading chimeric alignments from 'A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=11214293)
[2026-05-28T22:44:54] Marking multi-mapping alignments (marked=7484587)
[2026-05-28T22:44:59] Detecting strandedness (reverse)
[2026-05-28T22:44:59] Assigning strands to alignments 
[2026-05-28T22:45:01] Annotating alignments 
[2026-05-28T22:45:41] Filtering duplicates (remaining=8106848)
[2026-05-28T22:45:51] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=7536636)
[2026-05-28T22:45:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7536636)
[2026-05-28T22:45:55] Filtering viral contigs with expression lower than the top 5 (remaining=7536636)
[2026-05-28T22:46:01] Filtering viral contigs with less than 5% coverage (remaining=7536636)
[2026-05-28T22:46:03] Estimating fragment length (mate gap mean=-84.3972, mate gap stddev=29.6899, read length mean=127.637)
[2026-05-28T22:46:03] Filtering read-through fragments with a distance <=10000bp (remaining=7177038)
[2026-05-28T22:46:06] Filtering inconsistently clipped mates (remaining=7054001)
[2026-05-28T22:46:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6753693)
[2026-05-28T22:46:13] Filtering fragments with small insert size (remaining=6752328)
[2026-05-28T22:46:15] Filtering alignments with long gaps (remaining=6752327)
[2026-05-28T22:46:18] Filtering fragments with both mates in the same gene (remaining=6751089)
[2026-05-28T22:46:20] Filtering fusions arising from hairpin structures (remaining=6373865)
[2026-05-28T22:46:23] Filtering reads with a mismatch p-value <=0.01 (remaining=3051025)
[2026-05-28T22:46:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1233270)
[2026-05-28T22:46:52] Finding fusions and counting supporting reads (total=980692)
[2026-05-28T22:47:13] Merging adjacent fusion breakpoints (remaining=974516)
[2026-05-28T22:47:16] Filtering multi-mapping fusions by alignment score and read support (remaining=601623)
[2026-05-28T22:47:53] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T22:48:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=599012)
[2026-05-28T22:48:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=384414)
[2026-05-28T22:48:06] Filtering fusions with <2 supporting reads (remaining=33554)
[2026-05-28T22:48:07] Filtering fusions with an e-value >=0.3 (remaining=6921)
[2026-05-28T22:48:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6975)
[2026-05-28T22:48:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6866)
[2026-05-28T22:48:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6869)
[2026-05-28T22:48:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6481)
[2026-05-28T22:48:26] Searching for fusions with spliced split reads (remaining=6493)
[2026-05-28T22:48:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=4147)
[2026-05-28T22:48:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4100)
[2026-05-28T22:48:37] Searching for fusions with >=4 spliced events (remaining=5262)
[2026-05-28T22:48:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2441)
[2026-05-28T22:48:59] Filtering fusions with anchors <=23nt (remaining=1959)
[2026-05-28T22:49:00] Filtering end-to-end fusions with low support (remaining=1922)
[2026-05-28T22:49:01] Filtering fusions with no coverage around the breakpoints (remaining=1902)
[2026-05-28T22:49:02] Indexing gene sequences 
[2026-05-28T22:49:11] Filtering genes with >=30% identity (remaining=590)
[2026-05-28T22:49:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=272)
[2026-05-28T22:49:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=208)
[2026-05-28T22:49:26] Searching for additional isoforms (remaining=282)
[2026-05-28T22:49:27] Assigning confidence scores to events 
[2026-05-28T22:49:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T22:49:33] Writing fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T22:49:36] Writing discarded fusions to file 'A673_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T22:50:20] Freeing resources
[2026-05-28T22:50:43] Done (elapsed time=00:14:33, CPU time=00:14:32, peak memory=16gb)